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Dataset results
219 results for “molecular investigation”
Molecular investigation of bacterial communities on two frequently used surfaces in the São Paulo institute of tropical medicine
<p>In this study, we aimed to investigate the overall bacterial population on two frequently used surfaces in the São Paulo institute of tropical medicine (ITM) using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. The massive parallel sequencing data presented here were derived from the surface samples collected from restroom surfaces and the fingerprint door clock system (FDLS) in our ITM in São Paulo.</p>
Design and assembly of core/shell nanostructures as investigated by microfluidics and molecular dynamics simulation_dataset_DLS_TEM_MD
<p><span>He we like to publish data related to modified and non-modified MSN cores analysed using microfluidics platform against acetalated dextran (AcDEX)/spermine modified acetalated dextran (SpAcDEX) polymers. </span></p> <p><span>The data contains Dynamic light scattering (DLS) and TEM images which help us to to the demarcation of combinations which formed successful core/shell particles along with, <em>in-silico</em> modelling and molecular dynamics (MD) simulations data showing molecular interactions between the core particles and <a>the encapsulant </a></span><span><span></span></span><span>polymer. </span></p>
Surface science and liquid phase investigations of oxanorbornadiene/oxaquadricyclane ester derivatives as molecular solar thermal energy storage systems on Pt(111) [doi: 10.1063/5.0158124]
<p>Primary data, meta data, and corresponding lists of figures & tables are included. [doi: 10.1063/5.0158124]</p>
Advanced Molecular Dynamics Model for Investigating Biological-Origin Microfibril Structures
<p>This data contains all necessary input file to construct the micro fibril.</p>
Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii (nucleotide alignment dataset)
<p>This dataset includes the nucleotide alignment of eight Toxoplasma gondii genome loci (Sag1 / Chromossome VIII, Gra6 / Chromossome X, PK1 / Chromossome VI, Sag3 / Chromossome XII, L363 / Chromossome VIIb, CB21-4 / Chromossome III, M102 / Chromossome VIIa, Sag2 / Chromossome VIII). Each alignment includes sequences from T. gondii reference strains (retrieved from ToxoDB) as well as sequences from multiple clinical strains (obtained by Sanger / Next-generation sequencing) of the collection of the National Reference Laboratory of Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Portugal. </p>
Fig. 1 in Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species
Fig. 1. Sample sites location in the Paraná and Tietê rivers, state of São Paulo, Brazil.
Investigation of the behavior of dioxadet molecules in water by molecular dynamics
<p>A set of files for all-atom molecular dynamic simulations of a dioxadet molecule in water for four parametrizations obtained with a number of tools: ATBuilder, Amber tools, and Swiss Parameters.</p>
Data from: Small, but mitey: investigating the molecular genetic basis for mite domatia development and intraspecific variation in Vitis riparia using transcriptomics
Open the record for dataset details and reuse information.
Data for "Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition"
<p>Data for "Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition".</p> <p>neutron_data.zip --> neutron data in .nxspe form. S(Q,E) calculated using the DAVE software. Includes logbook spreadsheet. </p> <p>Training_Data.xyz --> xyz file containing training data used to generate Allegro machine learning forcefield in the paper</p> <p>nh3_pimd.deploy --> Trained Allegro model to that can be used in LAMMPS and RXMD software a ML forcefield </p> <p>POSCAR_UNIT_CELL_AMMONIA --> NH3 unit cell in solid phase in POSCAR format that can be read by the VASP software used to perform the DFT simmulations.</p>
FIGURE 2 in Molecular investigation of the intra-specific genetic variation in Plantago ovata Forssk. (Plantaginaceae): An insight into potential ancestral area distribution and probable time of dispersal versus vicariance events
FIGURE 2 Combined RASP and chronological tree of BEAST for P. ovata accessions (The scale numbers are in MY).
FIGURE1 in Molecular investigation of the intra-specific genetic variation in Plantago ovata Forssk. (Plantaginaceae): An insight into potential ancestral area distribution and probable time of dispersal versus vicariance events
FIGURE1 TCS network of the studied P. ovata plants based on ITS sequences showing a higher level of nucleotide replacement within the Asiatic samples (Hatch marks indicate the number of mutations).
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
<p>Dataset relative to Molecular dynamics simulation performed for the work "Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction".<br><br>The dataset contains data of 42 alchemical simulations and is subdivided in 4 zip files.<br><br>Folders are named following the scheme: system_configuration_forcefield.<br>Zip file C1 contains .mdp files used for all the simulations.<br><br>Folders corresponding to simulations performed with the fit5_AC ff contains:<br>- topology files (topol.top, topol_RNA_chain_A.itp, topol_RNA_chain_B.itp)<br>- index files needed to reconstruct the demuxed trajectories (replica_index.xvg , replica_index.xvg)<br>- 16 folders, one for each replica (lam0 ... lam15), containing:<br> - final configuration (confout.gro)<br> - log file (md.log)</p> <p> - input file for md run (md.tpr)<br> - energies for the concatenated trajectories recomputed for the realtive replica hamiltonian (ener_trj_conc.edr)<br><br>Folders corresponding to simlations performed with fit_A parametrization only contains .edr files corresponding to energies for the concatenated trajectory computed for 14 set of DeQs drawn from a gaussian distribution, with the relative topologies.<br><br>Supplementary materials relative to simlations performed with fit_A parametrizationcan be found in: https://zenodo.org/records/6498021</p>
Experimental microwave spectroscopic and quantum-chemical investigation of the HCl(H2O)n (n=1-5,7) molecular clusters
<p>In this dataset, experimental microwave rotational spectroscopy data and corresponding theoretical calculations for the HCl(H2O)n (n=1-5,7) clusters are stored. </p>
Data for "Investigating molecular transport in the human brain from MRI with physics-informed neural networks"
<p>Data analyzed in Zapf <em>et al.</em> <a href="https://www.nature.com/articles/s41598-022-19157-w">Investigating molecular transport in the human brain from MRI with physics-informed neural networks</a> (Scientific Reports 2022).</p> <p>The data consists of CSF tracer concentrations in the brain subregions analyzed in the article. The data was pre-processed as described in S1.1 in the supplementarty materials. </p> <p>In Python, load the data as numpy arrays using the nibabel package as</p> <pre><code>import nibabel data = nibabel.load("068/concentrations/24h.mgz").get_fdata() domain_mask = nibabel.load("068/masks/roi.mgz").get_fdata().astype(bool)<br>And view slices of the data as:</code></pre> <div> <div><span>plt</span><span>.</span><span>figure</span><span>()</span></div> <div><span>plt</span><span>.</span><span>imshow</span><span>(</span><span>np</span><span>.take(</span><span>data</span><span>, </span><span>150</span><span>, </span><span>0</span><span>), </span><span>vmax</span><span>=</span><span>0.1</span><span>)</span></div> <div><span>plt</span><span>.</span><span>figure</span><span>()</span></div> <div><span>plt</span><span>.</span><span>imshow</span><span>(</span><span>np</span><span>.take(</span><span>data</span><span>, </span><span>100</span><span>, </span><span>1</span><span>), </span><span>vmax</span><span>=</span><span>0.1</span><span>)</span></div> <div><span>plt</span><span>.</span><span>figure</span><span>()</span></div> <div><span>plt</span><span>.</span><span>imshow</span><span>(</span><span>np</span><span>.take(</span><span>data</span><span>, </span><span>100</span><span>, </span><span>2</span><span>), </span><span>vmax</span><span>=</span><span>0.1</span><span>)</span></div> <div><span>plt</span><span>.</span><span>show</span><span>()</span></div> </div> <pre> </pre>
The molecular investigation of Blood cockles (Anadara granosa) associated bacterial communities using 16S rRNA sequencing
<p>This data on the bacterial communities and its diversity associated with <em>Anadara granosa</em>. The <em>Anadara granosa</em> samples were obtained from two major estuaries in Penang, Malaysia using a culture dependent and 16S rRNA sequencing approach.</p>
FIGURE 8 in Morphological and molecular systematic investigation of Laurencia karachiana sp. nov. (Ceramiales, Rhodophyta) from Karachi, Pakistan
FIGURE 8. Holotype of Laurencia platyclada (NY00900238). The image belongs to The C.V. Starr Virtual Herbarium (http://sweetgum. nybg.org/science/vh/)
FIGURE 6 in Morphological and molecular systematic investigation of Laurencia karachiana sp. nov. (Ceramiales, Rhodophyta) from Karachi, Pakistan
FIGURE 6. Laurencia karachiana Bibi, Cassano & Rasheed sp. nov. (A) Female branches. (B) Detail of the branchlets showing cystocarps disposed subapically. (C) Longitudinal section through female branchlet with prominent cystocarp without protuberant ostiole. (D) Procarp-bearing segment with five pericentral cells, the fifth becoming the supporting cell (SU) of carpogonial branch; central cell of procarp-bearing segment (c), lateral sterile group (ls). (E) Development of young procarp; basal cell of trichoblast (bt) which supports the procarp; central cell of procarp-bearing segment (c) with five pericentral cells. (F) Procarp before fertilization with four-celled carpogonial branch (cb), carpogonium (cg), trichogyne (tr, unfocused), supporting cell (SU), lateral sterile group (ls), basal sterile group (bs). Scale bar: A, 2 mm; B, 1 mm; C, 200 μm; D-F, 10 mm.
FIGURE 7 in Morphological and molecular systematic investigation of Laurencia karachiana sp. nov. (Ceramiales, Rhodophyta) from Karachi, Pakistan
FIGURE 7. Laurencia karachiana Bibi, Cassano & Rasheed sp. nov. (A) Tetrasporangial branches. (B) Detail of tetrasporangial branchlets. (C) Transverse section of tetrasporangial axial segment showing axial cell (a) and two fertile pericentral cells, the third and fourth (arrows); the other two pericentral cells remain vegetative (p). (D) Detail of fertile pericentral cell (fp) with two pre-sporangial cover cells (pr), tetrasporangium (te); post-sporangial cover cell (po). (E) Longitudinal section through apical portion of tetrasporangial branchlet showing origin of tetrasporangia (te) from axial cell (arrow), fertile pericentral cells (fp) and pre-sporangial cover cells (pr). (F) Longitudinal section through a tetrasporangial branchlet showing parallel arrangement of tetrasporangia. Scale bar: A, 2 mm; B, 1 mm; C-E, 25 μm; F, 100 μm.
FIGURE 4 in Morphological and molecular systematic investigation of Laurencia karachiana sp. nov. (Ceramiales, Rhodophyta) from Karachi, Pakistan
FIGURE 4. Laurencia karachiana Bibi, Cassano & Rasheed sp. nov. (A) Habit of male gametophyte (Holotype KUH-SW-1312). (B) Habit of female gametophyte (Isotype SPF58339). (C) Habit of tetrasporophyte (Isotype SPF58339). (D) Detail of basal portion of the thallus showing discoid holdfast. (E) Cortical cells in surface view showing corps en cerise (one per cell) in living material. (F) Cortical cells in surface view showing secondary pit-connections (arrow). (F) Transverse section of thallus. Scale bar: A, 1 cm; B and C, 2 cm; D, 2 mm; E-F, 50 μm; G, 100 μm.
FIGURE 5 in Morphological and molecular systematic investigation of Laurencia karachiana sp. nov. (Ceramiales, Rhodophyta) from Karachi, Pakistan
FIGURE 5. Laurencia karachiana Bibi, Cassano & Rasheed sp. nov. (A) Transverse section of upper portion of branch showing an axial cell (arrow) with four pericentral cells (p). (B) Detail of medullary cell with lenticular thickening (arrow). (C) Male branches. (D) Detail of compound-cymose male branches. (E) Longitudinal section through a male branchlet showing spermatangial branches in cup-shaped tips. (F) Detail of of trichoblast-type spermatangial branches with two laterals, sterile (arrow) and spermatangial branches. (G) Detail of spermatangial branches with terminal vesicular sterile cells (arrow) and spermatangia with an apical nucleus. Scale bar: A and B, F and G, 25 μm; C, 2 mm; D, 1 mm; E, 100 μm.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.